GEO DataSets

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Mus musculus; human gut metagenome

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL19057 GPL29483

52 Samples

Download data

(Submitter supplied) Changes in microbiome composition have been associated with a wide array of human diseases, turning the human microbiota into an attractive target for therapeutic intervention. Yet clinical translation of these findings requires the establishment of causative connections between specific microbial taxa and their functional impact on host tissues. Here, we infused gut organ cultures with longitudinal microbiota samples collected from therapy-naïve irritable bowel syndrome (IBS) patients under low-FODMAP (fermentable Oligo-, Di-, Mono-saccharides and Polyols) diet. more...

Organism:

human gut metagenome

Type:

Other

Platform:

GPL29483

29 Samples

Download data: XLSX

(Submitter supplied) Gut microbial profiling of uterine fibroids (UFs) patients comparing control subjects. The gut microbiota was examined by 16S rRNA quantitative arrays and bioinformatics analysis. The goal was to reveal alterations in the gut microbiome of uterine fibroids patients.

Organism:

human feces metagenome; synthetic construct; human gut metagenome

Type:

Other

Platform:

GPL32019

85 Samples

Download data: TXT

(Submitter supplied) Crohn’s Disease (CD) pathogenesis is still unclear. Disorders in the mucosal immunoregulation and its crosstalk with the microbiota may represent an important component in tissue injury. We aimed to characterize the molecular immune response distribution within the ileal layers ( mucosa, submucosa and serosa) and to evaluate the correlated microbiota in pathological/healthy settings comparing first surgery/relapse clinical conditions.

Organism:

human gut metagenome

Type:

Other

Platform:

GPL29483

20 Samples

Download data: FASTA, TXT

(Submitter supplied) Here we report the 16S rRNA sequencing results of human fetal tissues, to identify bacterial genera present in developing fetus.

Organism:

human gut metagenome

Type:

Other

Platform:

GPL29896

294 Samples

Download data: CSV

(Submitter supplied) Familial Mediterranean fever (FMF) is an inflammatory genetic disease characterized by elevated systemic reactivity against commensal gut microbiota and high levels of gut Candida albicans. The current study investigated the effects of Lactobacillus acidophillus INMIA 9602 Er 317/402 strain (probiotic “Narine”) on the relative abundance of gut enteric bacteria, lactobacilli, Staphylococcus aureus, and Enteroccocus faecalis in Candida albicans-carrier and non-carrier FMF patients in remission with the main MEFV mutation patterns M694V/V726A- the prevalent MEFV gene mutation within FMF patients in the Armenian cohort. more...

Organism:

Archaea; Bacteria; human gut metagenome

Type:

Other

Platform:

GPL24736

166 Samples

Download data: CEL, TXT, XLSX

(Submitter supplied) Hundreds of microbial species were found to be transcriptionally active in the human gut microbiome based on the expression profiling of ca. 680.000 microbial genes

Organism:

human gut metagenome

Type:

Expression profiling by array

Platform:

GPL21303

233 Samples

Download data: XYS

(Submitter supplied) Significant gut microbiota heterogeneity exists amongst UC patients though the clinical implications of this variance are unknown. European and South Asian UC patients exhibit distinct disease risk alleles, many of which regulate immune function and relate to variation in gut microbiota β-diversity. We hypothesized ethnically distinct UC patients exhibit discrete gut microbiotas with unique luminal metabolic programming that influence adaptive immune responses and relate to clinical status. more...

Organism:

human gut metagenome; Bacteria; Archaea

Type:

Other

Platform:

GPL21523

34 Samples

Download data: CEL

(Submitter supplied) The protocol to test the preservation capabilities was based on a standardized procedure using the ECSIM, a chemostat-based fermentation system establishes to maintain microbiota. The initial fresh stool sample (1 g) was first cultivated in 5 mL, then 100 mL and then 1 L of a standard artificial gut medium and then either immediately tested in the P-ECSIM or preserved for 3 and 6 months with cryoprotectants before being next used for inoculation of the P-ECSIM. more...

Organism:

uncultured bacterium; human gut metagenome

Type:

Other

Platform:

GPL16731

15 Samples

Download data: TXT

(Submitter supplied) This study in rats was designed to investigate whether whole rhye (WR) can influence the metabolism of n-3 and n-6 long-chain fatty acids (LCFA) and gut microbiota composition. For 12 weeks, rats were fed a diet containing either 50% WR or 50% refined rye (RR). Total bacterial DNA was extracted from fecal and cecal samples (n=5 per group). 16S PCR amplification was performed to assess the microbial diversity at the family level using the HuGChip. more...

Organism:

human gut metagenome; uncultured bacterium

Type:

Expression profiling by array

Platform:

GPL20773

30 Samples

Download data: TXT

(Submitter supplied) Sequencing of 16S ribosomal RNA (rRNA) gene, which has improved the characterization of microbial community, has made it possible to detect a low level Helicobacter pylori (HP) sequences even in HP-negative subjects which were determined by a combination of conventional methods. This study was conducted to obtain a cutoff value for HP colonization in gastric mucosa biopsies and gastric juices by the pyrosequencing method. more...

Organism:

human gut metagenome

Type:

Other

Platform:

GPL20020

101 Samples

Download data: TXT

(Submitter supplied) We used a DNA microarray chip covering 369 resistance types to investigate the relation of antibiotic resistance gene diversity with humans’ age. Metagenomic DNA from fecal samples of 123 healthy volunteers of four different age groups, i.e. pre-school Children (CH), School Children (SC), High School Students (HSS) and Adults (AD) were used for hybridization. The results showed that 80 different gene types were recovered from the 123 individuals gut microbiota, among which 25 were present in CH, 37 in SC, 58 in HSS and 72 in AD. more...

Organism:

human gut metagenome; gut metagenome

Type:

Genome variation profiling by array

Platform:

GPL18168

123 Samples

Download data: PAIR

(Submitter supplied) Long-term dietary intake influences the structure and activity of the trillions of microorganisms residing in the human gut, but it remains unclear how rapidly and reproducibly the human gut microbiome responds to short-term macronutrient change. Here we show that the short-term consumption of diets composed entirely of animal or plant products alters microbial community structure and overwhelms inter-individual differences in microbial gene expression. more...

Organism:

human gut metagenome

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15595

59 Samples

Download data: TXT

(Submitter supplied) Distal gut bacteria play a pivotal role in the digestion of dietary polysaccharides by producing a large number of carbohydrate-active enzymes (CAZymes) that the host otherwise does not produce. We report here the design of a high density custom microarray that we used to spot non-redundant DNA probes for more than 6,500 genes encoding glycoside hydrolases and lyases selected from 174 reference genomes from distal gut bacteria. more...

Organism:

human gut metagenome

Type:

Genome variation profiling by array

Platform:

GPL17807

8 Samples

Download data: TXT

(Submitter supplied) We developed a non-invasive ex vivo HT29 cell-based minimal model to fingerprint the mucosa-associated microbiota fraction in humans. HT29 cell-associated fractions were characterized by the universal phylogenetic array platform HTF-Microbi.Array, both in presence or in absence of a TNF-α-mediated pro-inflammatory stimulus.

Organism:

synthetic construct; human gut metagenome

Type:

Other

Platform:

GPL17770

90 Samples

Download data: CSV

(Submitter supplied) A three-stage continuous fermentative system was developed to simulate and control physicochemical factors of the gut biology. Inoculation was of each reactor was performed from a human fecal sample which was initially amplified with a batch procedure. Samples from the initial feces, the batch and from the bioreactors media were collected to extract bacterial DNA. 16S PCR amplification was performed to assess the microbial diversity at the family level using the HuGChip. more...

Organism:

uncultured bacterium; human gut metagenome

Type:

Expression profiling by array

Platform:

GPL16731

5 Samples

Download data: TXT

(Submitter supplied) Microbiota from rats fed with wheat aleurone and plant omega fatty acids In this study we investigated how an AX-rich WA and ALA from linseed oil (LO) modulate the gut microbiota of rats. Wistar rats were fed a standard diet and received either an iso-energetic control oil (PO), control oil + aleurone (A+PO), linseed oil (LO) or linseed oil + aleurone (A+LO) during 12 weeks. Feacal samples were recovered after the 12 week treatments. more...

Organism:

Rattus norvegicus; human gut metagenome

Type:

Other

Platform:

GPL16731

25 Samples

Download data: TXT

(Submitter supplied) A phylogenetic microarray targeting 66 families described in the human gut microbiota has been developped aud used to monitor the gut microbiota's structure and diversity. The microarray format provided by Agilent and used in this study is 8x15K. A study with a total of 4 chips was realized.

Organism:

Lactobacillus acidophilus; human gut metagenome; Escherichia coli; Blautia coccoides; [Clostridium] leptum; Bacteroides fragilis; uncultured bacterium

Type:

Expression profiling by array

Platform:

GPL16731

4 Samples

Download data: TXT

(Submitter supplied) The human gut is colonized by trillions of microorganisms that influence human health and disease through the metabolism of xenobiotics, including therapeutic drugs and antibiotics. The diversity and metabolic potential of the human gut microbiome have been extensively characterized, but it remains unclear which microorganisms are active and which perturbations can influence this activity. Here, we use flow cytometry, 16S rRNA gene sequencing, and metatranscriptomics to demonstrate that the human gut contains distinctive subsets of active and damaged microorganisms, primarily composed of Firmicutes, which display marked temporal variation. more...

Organism:

human gut metagenome

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15595

72 Samples

Download data: TXT

(Submitter supplied) Understanding how the human gut microbiota and host are impacted by probiotic bacterial strains requires carefully controlled studies in humans, and in mouse models of the gut ecosystem where potentially confounding variables that are difficult to control in humans can be constrained. Therefore, we characterized the fecal microbiomes and metatranscriptomes of adult female monozygotic twin pairs through repeated sampling 4 weeks prior to, 7 weeks during, and 4 weeks following consumption of a commercially-available fermented milk product (FMP) containing a consortium of Bifidobacterium animalis subsp. more...

Organism:

Lactobacillus; Lactobacillus delbrueckii subsp. bulgaricus; human gut metagenome; Bifidobacterium animalis subsp. lactis CNCM I-2494; Streptococcus thermophilus CNCM I-1630; Ruminococcus; Bacteroides; Collinsella; Streptococcus thermophilus; Clostridia; Parabacteroides; Lactococcus lactis subsp. lactis CNCM I-1631

Type:

Expression profiling by high throughput sequencing

4 related Platforms

73 Samples

Download data: TXT